| name | foldmason |
| description | FoldMason — multiple protein structure alignment at scale (Steinegger lab). Use when: (1) Building structural MSAs from AFDB / predicted models, (2) Comparing folds across MAG protein families after Foldseek clustering, (3) Preparing structure-aware alignments for phylogeny or motif work. Upstream: https://github.com/steineggerlab/foldmason. Web: https://search.foldseek.com/foldmason. Route via homology-search.
|
| license | MIT |
| category | analysis-tools |
| tags | ["FoldMason","structure-MSA","Foldseek","alignment"] |
| upstream | https://github.com/steineggerlab/foldmason |
| stage | function |
FoldMason
Upstream: steineggerlab/foldmason ·
Web: https://search.foldseek.com/foldmason
Citation
Gilchrist, C. L. M., Mirdita, M. & Steinegger, M. Multiple protein structure
alignment at scale with FoldMason. Science 391, 485–488 (2026).
https://doi.org/10.1126/science.ads6733
See also docs/references.md.
Analytical thinking
Foldseek finds pairwise structural neighbors; FoldMason builds scalable
multiple structure alignments (FASTA + HTML reports). Useful after
clustering dark proteins or AFDB hits into families.
| vs | Prefer FoldMason when |
|---|
foldseek | Need MSA of many structures, not just hit table |
| Sequence MSA (MAFFT/…) | Structures available / twilight zone |
folddisco | Global structural MSA vs local motif |
How to run
conda install -c bioconda foldmason
foldmason easy-msa structures/*.pdb result.fasta tmp --report-mode 1
Decision tree
Have a set of related structures?
├─ Pairwise search only → foldseek
├─ Multiple structure alignment → foldmason
├─ Short motif → folddisco
└─ Sequence MSA → hh-suite / classical aligners
Related skills
foldseek · folddisco · foldcomp · unicore · homology-search ·
phylogenomics · tool-selection
